BioMOBY Registry Scripts

The BioMOBY registry scripts are a required install for all you wishing to host your very own BioMOBY registry. These scripts contain the code that is used to retrieve information regarding the ontologies in RDF format, code for generating RDF that is served to the service providers upon successful service registration, an LSID resolution authority, and much more.

The following is a list of items contained in this release:

    1. RESOURCES - a script that is used to generate RDF dumps for the Object, Namespace, Service Type, and Service Instance ontologies.
    2. LSID Authority - a script that is used to resolve*, LSIDs to metadata.
    3. Service Tester - a script that periodically 'pings' the services contained in the registry to determine whether or not the services URL are resolvable.
    4. RDFAgent Validator - a form that can be used to test whether your installation of the agent was successful, or to test an RDF document that describes your services for syntactical errors.
    5. Service Pinger Validator - a form that can be used to ping individual services so that you can determine whether there is a problem with that particular service.
    6. Service Instance RDF Generator - a form that can be used to generate RDF for any pre-registered service, or a group of services, in the registry.
This document is broken down into the following sections:


Installing the Scripts

Installing the scripts are extremely straight-forward and quite easy.

Installation Procedure

      1. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.

      2. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/

      3. Copy the following files to your webservers cgi-bin directory

        Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron)


      4. You're done. All that is left for you to do is configure the newly installed scripts.

      Please make sure that the first line of all the scripts corresponds to the correct location of your perl executable.
      For instance if you perl is located in /bin/my/perl, then make sure to modify the first line of each of the scripts so that they read #!/bin/my/perl -w

Configuring Your Scripts

To Configure the servlets, you must know the following details regarding your local registry:

Testing Your Scripts

Once you have installed and configured the scripts, you can determine if the install was successful by attempting to resolve the following URL:

where is the domain name of the server that the servlets were installed on and your_port is the server port.

The resulting page will outline those scripts that are included in this distribution and will provide you with links to test them.

Edward A Kawas